Literature DB >> 29694873

Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance.

Maarten M van Oene1, Seungkyu Ha1, Tessa Jager1, Mina Lee1, Francesco Pedaci1, Jan Lipfert2, Nynke H Dekker3.   

Abstract

Single-molecule manipulation techniques have provided unprecedented insights into the structure, function, interactions, and mechanical properties of biological macromolecules. Recently, the single-molecule toolbox has been expanded by techniques that enable measurements of rotation and torque, such as the optical torque wrench (OTW) and several different implementations of magnetic (torque) tweezers. Although systematic analyses of the position and force precision of single-molecule techniques have attracted considerable attention, their angle and torque precision have been treated in much less detail. Here, we propose Allan deviation as a tool to systematically quantitate angle and torque precision in single-molecule measurements. We apply the Allan variance method to experimental data from our implementations of (electro)magnetic torque tweezers and an OTW and find that both approaches can achieve a torque precision better than 1 pN · nm. The OTW, capable of measuring torque on (sub)millisecond timescales, provides the best torque precision for measurement times ≲10 s, after which drift becomes a limiting factor. For longer measurement times, magnetic torque tweezers with their superior stability provide the best torque precision. Use of the Allan deviation enables critical assessments of the torque precision as a function of measurement time across different measurement modalities and provides a tool to optimize measurement protocols for a given instrument and application.
Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mesh:

Year:  2018        PMID: 29694873      PMCID: PMC5937147          DOI: 10.1016/j.bpj.2018.02.039

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  47 in total

1.  Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA.

Authors:  Florian C Oberstrass; Louis E Fernandes; Zev Bryant
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-02       Impact factor: 11.205

2.  Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments.

Authors:  Jan Lipfert; Jacob W J Kerssemakers; Tessa Jager; Nynke H Dekker
Journal:  Nat Methods       Date:  2010-10-17       Impact factor: 28.547

Review 3.  Direct measurement of torque in an optical trap and its application to double-strand DNA.

Authors:  László Oroszi; Péter Galajda; Huba Kirei; Sándor Bottka; Pál Ormos
Journal:  Phys Rev Lett       Date:  2006-08-01       Impact factor: 9.161

4.  Magnetic tweezers measurement of single molecule torque.

Authors:  Alfredo Celedon; Ilana M Nodelman; Bridget Wildt; Rohit Dewan; Peter Searson; Denis Wirtz; Gregory D Bowman; Sean X Sun
Journal:  Nano Lett       Date:  2009-04       Impact factor: 11.189

5.  The effect of integration time on fluctuation measurements: calibrating an optical trap in the presence of motion blur.

Authors:  Wesley P Wong; Ken Halvorsen
Journal:  Opt Express       Date:  2006-12-11       Impact factor: 3.894

6.  Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules.

Authors:  Scott Forth; Christopher Deufel; Maxim Y Sheinin; Bryan Daniels; James P Sethna; Michelle D Wang
Journal:  Phys Rev Lett       Date:  2008-04-08       Impact factor: 9.161

7.  Optical tweezers with millikelvin precision of temperature-controlled objectives and base-pair resolution.

Authors:  Mohammed Mahamdeh; Erik Schäffer
Journal:  Opt Express       Date:  2009-09-14       Impact factor: 3.894

Review 8.  Torque spectroscopy for the study of rotary motion in biological systems.

Authors:  Jan Lipfert; Maarten M van Oene; Mina Lee; Francesco Pedaci; Nynke H Dekker
Journal:  Chem Rev       Date:  2014-12-26       Impact factor: 60.622

9.  Torque spectroscopy of DNA: base-pair stability, boundary effects, backbending, and breathing dynamics.

Authors:  Florian C Oberstrass; Louis E Fernandes; Paul Lebel; Zev Bryant
Journal:  Phys Rev Lett       Date:  2013-04-25       Impact factor: 9.161

10.  Kinesin rotates unidirectionally and generates torque while walking on microtubules.

Authors:  Avin Ramaiya; Basudev Roy; Michael Bugiel; Erik Schäffer
Journal:  Proc Natl Acad Sci U S A       Date:  2017-09-25       Impact factor: 11.205

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  4 in total

1.  High-Resolution Photonic Force Microscopy Based on Sharp Nanofabricated Tips.

Authors:  Rudy Desgarceaux; Zhanna Santybayeva; Eliana Battistella; Ashley L Nord; Catherine Braun-Breton; Manouk Abkarian; Onofrio M Maragò; Benoit Charlot; Francesco Pedaci
Journal:  Nano Lett       Date:  2020-05-13       Impact factor: 11.189

2.  Versatile Multilayer Metamaterial Nanoparticles with Tailored Optical Constants for Force and Torque Transduction.

Authors:  Ying Tang; Seungkyu Ha; Thomas Begou; Julien Lumeau; H Paul Urbach; Nynke H Dekker; Aurèle J L Adam
Journal:  ACS Nano       Date:  2020-11-10       Impact factor: 15.881

3.  Tweezepy: A Python package for calibrating forces in single-molecule video-tracking experiments.

Authors:  Ian L Morgan; Omar A Saleh
Journal:  PLoS One       Date:  2021-12-31       Impact factor: 3.240

4.  Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque.

Authors:  Stepan Dzhimak; Alexandr Svidlov; Anna Elkina; Eugeny Gerasimenko; Mikhail Baryshev; Mikhail Drobotenko
Journal:  Int J Mol Sci       Date:  2022-04-17       Impact factor: 6.208

  4 in total

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